Hughes Mentor:  Jeffrey Doyle

Department: Plant Biology

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Interview with a Faculty Member- Jeff Doyle

When preparing to interview Jeff Doyle for the Howard Hughes Program I asked several people if they knew who he was. Surprisingly, almost everyone I asked not only knew him, but they went on to say that he was known for being a really good advisor. To be singled out in such a positive manner among the many Cornell professors is no small feat, and when I finally went to interview him I understood how he had gained such a reputation.

After a very friendly introduction, my first question was about his research itself. His passion for the topic was immediately apparent. He began to explain polyploidy in plants as I had never understood it. Polyploidy, he said, gives plants an evolutionary advantage because it allows for hybridity. Think of a donkey and a horse mating to make a mule. A mule itself is sterile, but if it could double its chromosome number it would be able to pass on its genes by pairing its two horse chromosomes together and its two donkey chromosomes together. The creation of hybrids in plants is a lot more common than in animals, and the doubling of their genome is an important step in the evolution of many plant species. Dr. Doyle went on to explain that his lab also analyzes a region of the soybean genome that is one million base pairs long and involved in disease resistance. His lab looks for evidence of genome flow in the soy bean family, as well as age and interaction of polyploidy among the different species related to the soybean.

I asked Dr. Doyle whether a genuine interest in plant evolution or a desire to help agriculture through basic research inspired him. He smiled at me as though he had been expecting the question and told me that both of these reasons and neither of these reasons inspired him. He went on to explain that it was curiosity and a love of students that inspired him. He talked about publishing as though it was completely secondary to the research that was going on in his lab. As far as applied research goes, he said that he had a grant to work on a biofuels project involving alfalfa. He joked that if you’re involved in basic research long enough, you end up doing something for the good of your fellow man just by chance.

Dr. Doyle did not set out to be a botanist. Rather, from a very young age he wanted be a herpetologist. His love of plants began to grow while he was hiking as a child trying to take pictures of reptiles. Because plants were much easier to find, he would also take pictures of interesting plants he saw along the way. When he set out to study herpetology at the university level, he received very bad mentorship from a herpetology faculty member and very good mentorship from a botany professor. He takes this a very important lesson in the importance in mentorship, and his passion for plants and teaching makes it very apparent that he is happy with the direction his research has taken him.

A Day in the Doyle Lab

We’re a nucleotide lab. Agarose gels run all day and thermocyclers must be signed up for in advance. But we’re also a plant lab, which may be the more defining characteristic. There’s a mild, caring temperament that comes with plant work, and I see it in all my colleagues. Perhaps it’s their fascination with the fluidity and constancy of the natural world, or simply the fact that plants don’t cry, they don’t whimper, and they don’t ever look up at you with sad, lost eyes. I like to think I share their wholly moral conscience, but in truth I’m not a plant guy by nature. With medical aspirations, I suspect this will be one of my last opportunities to work in such an environment. And I have found that after the often impersonal drain of daily life, it’s refreshing to meet people with such a profound respect for the natural world.

After a morning starbucks, I begin by either an RNA extraction from leaf tissue collected from the Cornell greenhouses, or I set up a polymerase chain reaction. I study cellulose synthase, the enzyme complex that synthesizes cellulose. Cellulose is the most abundant polymer on our plant, a major cell wall component of plants, and it molecule essential for the future of bioenergy. The cellulose synthase gene family is extensive in plants and I want to characterize it in two organisms I’ve selected, Medicago sativa (alfalfa) a prominent biofuels crop, and Glycine tomentella, from the soybean genus. I would like to study when and where the different cellulose synthase isoforms are expressed in order to gain some insight in the physiological function as well as the evolution of the enzyme complex. Ultimately, I’d like to apply these gene expression studies to polyploidy, that is, genome duplication. This is the major reason I chose to study G. tomentella. There is a 15 million year duplication, a 50,000 year duplication and a synthetic polyploid made in the lab. With this wide variety of ancient and recent polyploids, I can investigate how evolution and genome duplication has shaped the expression, and ultimately, the function of cellulose synthase.

Of course, as an undergraduate researcher, it often isn’t as much what you accomplish as what you learn. I’ve learned that research can be slow at times but that the most successful researchers are never overwhelmed by setbacks. An experiment is still a success even if it doesn’t give expected results and a clever scientist learns something from every experiment no matter what the outcome. Initially, to identify the cellulose synthase gene family I attempted to amplify and clone using conserved primers. I ended up, however, with over fifty different sequences, all putative cellulose synthase genes. But in truth, since expression patterns were what I was most interested in, I used my failure in genomic cloning to lead me in a new direction. I began cloning from RNA and therefore only obtained expressed sequences. This narrowed my results and gave me a more manageable gene tree and ultimately what looks like thirteen potential cellulose synthase gene expressed in G. tomentella diploids.

In the future I plan to continue cDNA cloning and make specific primers for as many cellulose synthase genes as possible. After that I can do gene expression studies for diploid and tetraploid accessions of my organisms of interest to gain some understanding of how polyploid and evolution has shaped the function of the enzyme that syntheses one of the most important and widespread compounds on our planet.

A Day in the Life of an Undergraduate Researcher

I work in Prof. Jeff Doyle’s lab, which studies plant biology. Before coming to this lab I had taken some classes on botany and plant evolution. These classes really helped me understand the concepts of my work. My classes in general biology and genetics also taught me a lot of useful background information. For the actual lab work, the class I took on biochemistry lab techniques was extremely helpful.

In the lab I am trying to find several gene sequences in soybean relatives. I do that by extracting the DNA from leaves by grinding them up and treating them with detergents and chloroform. Once I have the DNA, I do a polymerase chain reaction (PCR), which multiplies selected regions of DNA. Then I run the DNA out in a gel. This separates the selected regions from the rest of the DNA. I stain the DNA so it can be seen under UV light and then cut out the selected DNA. Next, I remove the DNA from the gel by adding chemicals and centrifuging. Finally, I send the DNA away for sequencing.

In my typical day, I do several PCR reactions, which takes a few hours. Then I run the PCR reactions from the previous day on a gel. I spend a lot of time repeating PCRs and gels in order to get good results. Each gene I sequence usually takes three or four tries before I get good results, and sometimes I have to repeat them even more. Occasionally, I extract DNA from plant leaves. This takes a whole day, but fortunately I get enough DNA to last for a lot of experiments. I also spend a fair amount of time on the computer, looking at DNA sequence. I have to look at several thousand bases to check that the computer read them properly.

I have learned a lot of new techniques while working in the lab, such as PCR, making gels, and DNA extraction. I have also learned a lot of good lab practices, like keeping supplies sterile and being careful with measurements. I have ruined several days worth of work just by dropping things or forgetting to add one chemical to my reactions. These mistakes have taught me to be especially careful. I have also learned how important it is to take good notes, since forgetting to write something down can make it much more difficult if I have to repeat my experiment later. My work in the lab has also taught me a bit about myself, as I found that I enjoy doing lab work, even though it can be very repetitive. It can be very frustrating to get poor results several times in a row, but it is very exciting when the experiment finally works. I am looking forward to continuing my work in the lab next year.